Soft robotics for farm to fork: applications in agriculture & farming.

Agricultural tasks and environments range from harsh field conditions with semi-structured produce or animals, through to post-processing tasks in food-processing environments. From farm to fork, the development and application of soft robotics offers a plethora of potential uses. Robust yet compliant interactions between farm produce and machines will enable new capabilities and optimize existing processes. There is also an opportunity to explore how modeling tools used in soft robotics can be applied to improve our representation and understanding of the soft and compliant structures common in agriculture. In this review, we seek to highlight the potential for soft robotics technologies within the food system, and also the unique challenges that must be addressed when developing soft robotics systems for this problem domain. We conclude with an outlook on potential directions for meaningful and sustainable impact, and also how our outlook on both soft robotics and agriculture must evolve in order to achieve the required paradigm shift.

Thrice out of Asia and the adaptive radiation of the western honey bee.

The origin of the western honey bee Apis mellifera has been intensely debated. Addressing this knowledge gap is essential for understanding the evolution and genetics of one of the world's most important pollinators. By analyzing 251 genomes from 18 native subspecies, we found support for an Asian origin of honey bees with at least three expansions leading to African and European lineages. The adaptive radiation of honey bees involved selection on a few genomic "hotspots." We found 145 genes with independent signatures of selection across all bee lineages, and these genes were highly associated with worker traits. Our results indicate that a core set of genes associated with worker and colony traits facilitated the adaptive radiation of honey bees across their vast distribution.

Defense Response in Brazilian Honey Bees (Apis mellifera scutellata × spp.) Is Underpinned by Complex Patterns of Admixture.

In 1957, an invasive and highly defensive honey bee began to spread across Brazil. In the previous year, Brazilian researchers hoped to produce a subtropical-adapted honey bee by crossing local commercial honey bees (of European origin) with a South African honey bee subspecies (Apis mellifera scutellata; an A-lineage honey bee subspecies). The resulting cross-African hybrid honey bees (AHBs)-escaped from their enclosure and spread through the Americas. Today, AHB is the most common honey bee from Northern Argentina to the Southern United States. AHBs are much more likely to sting nest intruders than managed European-derived honey bee colonies. Previous studies have explored how genetic variation contributes to differences in defense response between European-derived honey bee and AHB. Although this work demonstrated very strong genetic effects on defense response, they have yet to pinpoint which genes influence variation in defense response within AHBs, specifically. We quantified defense response for 116 colonies in Brazil and performed pooled sequencing on the most phenotypically divergent samples. We identified 65 loci containing 322 genes that were significantly associated with defense response. Loci were strongly associated with metabolic function, consistent with previous functional genomic analyses of this phenotype. Additionally, defense-associated loci had nonrandom and unexpected patterns of admixture. Defense response was not simply the product of more A-lineage honey bee ancestry as previously assumed, but rather an interaction between A-lineage and European alleles. Our results suggest that a combination of A-lineage and European alleles play roles in defensive behavior in AHBs.

Colonization history and population differentiation of the Honey Bees (Apis mellifera L.) in Puerto Rico.

Honey bees (Apis mellifera L.) are the primary commercial pollinators across the world. The subspecies A. m. scutellata originated in Africa and was introduced to the Americas in 1956. For the last 60 years, it hybridized successfully with European subspecies, previous residents in the area. The result of this hybridization was called Africanized honey bee (AHB). AHB has spread since then, arriving to Puerto Rico (PR) in 1994. The honey bee population on the island acquired a mosaic of features from AHB or the European honey bee (EHB). AHB in Puerto Rico shows a major distinctive characteristic, docile behavior, and is called gentle Africanized honey bees (gAHB). We used 917 SNPs to examine the population structure, genetic differentiation, origin, and history of range expansion and colonization of gAHB in PR. We compared gAHB to populations that span the current distribution of A. mellifera worldwide. The gAHB population is shown to be a single population that differs genetically from the examined populations of AHB. Texas and PR groups are the closest genetically. Our results support the hypothesis that the Texas AHB population is the source of gAHB in Puerto Rico.

Finding the missing honey bee genes: lessons learned from a genome upgrade.

BACKGROUND: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. RESULTS: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. CONCLUSIONS: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.

Genes associated with honey bee behavioral maturation affect clock-dependent and -independent aspects of daily rhythmic activity in fruit flies.

BACKGROUND: In the honey bee, the age-related and socially regulated transition of workers from in-hive task performance (e.g., caring for young) to foraging (provisioning the hive) is associated with changes in many behaviors including the 24-hour pattern of rhythmic activity. We have previously shown that the hive-bee to forager transition is associated with extensive changes in brain gene expression. In this study, we test the possible function of a subset of these genes in daily rhythmic activity pattern using neural-targeted RNA interference (RNAi) of an orthologous gene set in Drosophila melanogaster. PRINCIPAL FINDINGS: Of 10 genes tested, knockdown of six affected some aspect of locomotor activity under a 12 h:h light:dark regime (LD). Inos affected anticipatory activity preceding lights-off, suggesting a possible clock-dependent function. BM-40-SPARC, U2af50 and fax affected peak activity at dawn without affecting anticipation or overall inactivity (proportion of 15-min intervals without activity), suggesting that these effects may depend on the day-night light cycle. CAH1 affected overall inactivity. The remaining gene, abl, affected peak activity levels but was not clearly time-of-day-specific. No gene tested affected length of period or strength of rhythmicity in constant dark (DD), suggesting that these genes do not act in the core clock. SIGNIFICANCE: Taking advantage of Drosophila molecular genetic tools, our study provides an important step in understanding the large set of gene expression changes that occur in the honey bee transition from hive bee to forager. We show that orthologs of many of these genes influence locomotor activity in Drosophila, possibly through both clock-dependent and -independent pathways. Our results support the importance of both circadian clock and direct environmental stimuli (apart from entrainment) in shaping the bee's 24-hour pattern of activity. Our study also outlines a new approach to dissecting complex behavior in a social animal.

A genome-wide signature of positive selection in ancient and recent invasive expansions of the honey bee Apis mellifera.

Apis mellifera originated in Africa and extended its range into Eurasia in two or more ancient expansions. In 1956, honey bees of African origin were introduced into South America, their descendents admixing with previously introduced European bees, giving rise to the highly invasive and economically devastating "Africanized" honey bee. Here we ask whether the honey bee's out-of-Africa expansions, both ancient and recent (invasive), were associated with a genome-wide signature of positive selection, detected by contrasting genetic differentiation estimates (F(ST)) between coding and noncoding SNPs. In native populations, SNPs in protein-coding regions had significantly higher F(ST) estimates than those in noncoding regions, indicating adaptive evolution in the genome driven by positive selection. This signal of selection was associated with the expansion of honey bees from Africa into Western and Northern Europe, perhaps reflecting adaptation to temperate environments. We estimate that positive selection acted on a minimum of 852-1,371 genes or approximately 10% of the bee's coding genome. We also detected positive selection associated with the invasion of African-derived honey bees in the New World. We found that introgression of European-derived alleles into Africanized bees was significantly greater for coding than noncoding regions. Our findings demonstrate that Africanized bees exploited the genetic diversity present from preexisting introductions in an adaptive way. Finally, we found a significant negative correlation between F(ST) estimates and the local GC content surrounding coding SNPs, suggesting that AT-rich genes play an important role in adaptive evolution in the honey bee.

Species differences in brain gene expression profiles associated with adult behavioral maturation in honey bees.

BACKGROUND: Honey bees are known for several striking social behaviors, including a complex pattern of behavioral maturation that gives rise to an age-related colony division of labor and a symbolic dance language, by which successful foragers communicate the location of attractive food sources to their nestmates. Our understanding of honey bees is mostly based on studies of the Western honey bee, Apis mellifera, even though there are 9-10 other members of genus Apis, showing interesting variations in social behavior relative to A. mellifera. To facilitate future in-depth genomic and molecular level comparisons of behavior across the genus, we performed a microarray analysis of brain gene expression for A. mellifera and three key species found in Asia, A. cerana, A. florea and A. dorsata. RESULTS: For each species we compared brain gene expression patterns between foragers and adult one-day-old bees on an A. mellifera cDNA microarray and calculated within-species gene expression ratios to facilitate cross-species analysis. The number of cDNA spots showing hybridization fluorescence intensities above the experimental threshold was reduced by an average of 16% in the Asian species compared to A. mellifera, but an average of 71% of genes on the microarray were available for analysis. Brain gene expression profiles between foragers and one-day-olds showed differences that are consistent with a previous study on A. mellifera and were comparable across species. Although 1772 genes showed significant differences in expression between foragers and one-day-olds, only 218 genes showed differences in forager/one-day-old expression between species (p < 0.001). Principal Components Analysis revealed dominant patterns of expression that clearly distinguished between the four species but did not reflect known differences in behavior and ecology. There were species differences in brain expression profiles for functionally related groups of genes. CONCLUSION: We conclude that the A. mellifera cDNA microarray can be used effectively for cross-species comparisons within the genus. Our results indicate that there is a widespread conservation of the molecular processes in the honey bee brain underlying behavioral maturation. Species differences in brain expression profiles for functionally related groups of genes provide possible clues to the basis of behavioral variation in the genus.

Genome scan for cis-regulatory DNA motifs associated with social behavior in honey bees.

Honey bees (Apis mellifera) undergo an age-related, socially regulated transition from working in the hive to foraging, which is associated with changes in the expression of thousands of genes in the brain. To begin to study the cis-regulatory code underlying this massive social regulation of gene expression, we used the newly sequenced honey bee genome to scan the promoter regions of eight sets of behaviorally related genes differentially expressed in the brain in the context of division of labor among worker bees, for 41 cis-regulatory motifs previously characterized in Drosophila melanogaster. Binding sites for the transcription factors Hairy, GAGA, Adf1, Cf1, Snail, and Dri, known to function in nervous system development, olfactory learning, or hormone binding in Drosophila, were significantly associated with one or more gene sets. The presence of some binding sites also predicted expression patterns for as many as 71% of the genes in some gene sets. These results suggest that there is a robust relationship between cis and social regulation of brain gene expression, especially considering that we studied <15% of all known transcription factors. These results also suggest that transcriptional networks involved in the regulation of development in Drosophila are used to regulate behavioral development in adult honey bees. However, differences in gene regulation between these two processes are suggested by the finding that the promoter regions for the behaviorally related bee genes differed in both motif occurrence and G/C content relative to their Drosophila orthologs.

Genomic dissection of behavioral maturation in the honey bee.

Honey bees undergo an age-related, socially regulated transition from working in the hive to foraging that has been previously associated with changes in the expression of thousands of genes in the brain. To understand the meaning of these changes, we conducted microarray analyses to examine the following: (i) the ontogeny of gene expression preceding the onset of foraging, (ii) the effects of physiological and genetic factors that influence this behavioral transition, and (iii) the effects of foraging experience. Although >85% of approximately 5,500 genes showed brain differences, principal component analysis revealed discrete influences of age, behavior, genotype, environment, and experience. Young bees not yet competent to forage showed extensive, age-related expression changes, essentially complete by 8 days of age, coinciding with previously described structural brain changes. Subsequent changes were not age-related but were largely related to effects of juvenile hormone (JH), suggesting that the increase in JH that influences the hive bee-forager transition may cause many of these changes. Other treatments that also influence the onset age of foraging induced many changes but with little overlap, suggesting that multiple pathways affect behavioral maturation. Subspecies differences in onset age of foraging were correlated with differences in JH and JH-target gene expression, suggesting that this endocrine system mediates the genetic differences. We also used this multifactorial approach to identify candidate genes for behavioral maturation. This successful dissection of gene expression indicates that, for social behavior, gene expression in the brain can provide a robust indicator of the interaction between hereditary and environmental information.

Thrice out of Africa: ancient and recent expansions of the honey bee, Apis mellifera.

We characterized Apis mellifera in both native and introduced ranges using 1136 single-nucleotide polymorphisms genotyped in 341 individuals. Our results indicate that A. mellifera originated in Africa and expanded into Eurasia at least twice, resulting in populations in eastern and western Europe that are geographically close but genetically distant. A third expansion in the New World has involved the near-replacement of previously introduced "European" honey bees by descendants of more recently introduced A. m. scutellata ("African" or "killer" bees). Our analyses of spatial transects and temporal series in the New World revealed differential replacement of alleles derived from eastern versus western Europe, with admixture evident in all individuals.

Semiparametric approach to characterize unique gene expression trajectories across time.

BACKGROUND: A semiparametric approach was used to identify groups of cDNAs and genes with distinct expression profiles across time and overcome the limitations of clustering to identify groups. The semiparametric approach allows the generalization of mixtures of distributions while making no specific parametric assumptions about the distribution of the hidden heterogeneity of the cDNAs. The semiparametric approach was applied to study gene expression in the brains of Apis mellifera ligustica honey bees raised in two colonies (A. m. mellifera and ligustica) with consistent patterns across five maturation ages. RESULTS: The semiparametric approach provided unambiguous criteria to detect groups of genes, trajectories and probability of gene membership to groups. The semiparametric results were cross-validated in both colony data sets. Gene Ontology analysis enhanced by genome annotation helped to confirm the semiparametric results and revealed that most genes with similar or related neurobiological function were assigned to the same group or groups with similar trajectories. Ten groups of genes were identified and nine groups had highly similar trajectories in both data sets. Differences in the trajectory of the reminder group were consistent with reports of accelerated maturation in ligustica colonies compared to mellifera colonies. CONCLUSION: The combination of microarray technology, genomic information and semiparametric analysis provided insights into the genomic plasticity and gene networks linked to behavioral maturation in the honey bee.

The enduring effects of abuse and related adverse experiences in childhood. A convergence of evidence from neurobiology and epidemiology.

BACKGROUND: Childhood maltreatment has been linked to a variety of changes in brain structure and function and stress-responsive neurobiological systems. Epidemiological studies have documented the impact of childhood maltreatment on health and emotional well-being. METHODS: After a brief review of the neurobiology of childhood trauma, we use the Adverse Childhood Experiences (ACE) Study as an epidemiological "case example" of the convergence between epidemiologic and neurobiological evidence of the effects of childhood trauma. The ACE Study included 17,337 adult HMO members and assessed 8 adverse childhood experiences (ACEs) including abuse, witnessing domestic violence, and serious household dysfunction. We used the number of ACEs (ACE score) as a measure of cumulative childhood stress and hypothesized a "dose-response" relationship of the ACE score to 18 selected outcomes and to the total number of these outcomes (comorbidity). RESULTS: Based upon logistic regression analysis, the risk of every outcome in the affective, somatic, substance abuse, memory, sexual,and aggression-related domains increased in a graded fashion as the ACE score increased (P <0.001). The mean number of comorbid outcomes tripled across the range of the ACE score. CONCLUSIONS: The graded relationship of the ACE score to 18 different outcomes in multiple domains theoretically parallels the cumulative exposure of the developing brain to the stress response with resulting impairment in multiple brain structures and functions.

Adverse childhood experiences and hallucinations.

OBJECTIVE: Little information is available about the contribution of multiple adverse childhood experiences (ACEs) to the likelihood of reporting hallucinations. We used data from the ACE study to assess this relationship. METHODS: We conducted a survey about childhood abuse and household dysfunction while growing up, with questions about health behaviors and outcomes in adulthood, which was completed by 17,337 adult HMO members in order to assess the independent relationship of 8 adverse childhood experiences and the total number of ACEs (ACE score) to experiencing hallucinations. We used logistic regression to assess the relationship of the ACE score to self-reported hallucinations. RESULTS: We found a statistically significant and graded relationship between histories of childhood trauma and histories of hallucinations that was independent of a history of substance abuse. Compared to persons with 0 ACEs, those with 7 or more ACEs had a five-fold increase in the risk of reporting hallucinations. CONCLUSION: These findings suggest that a history of childhood trauma should be looked for among persons with a history of hallucinations.

Long-term consequences of childhood sexual abuse by gender of victim.

BACKGROUND: Childhood sexual abuse (CSA) is a worldwide problem. Although most studies on the long-term consequences of CSA have focused on women, sexual abuse of both boys and girls is common. Thus, a comparison of the long-term effects of CSA by gender of the victim will provide perspective on the need for future research, prevention activities, and treatment of survivors. METHODS: A retrospective cohort study was conducted from 1995 to 1997 among 17,337 adult HMO members in San Diego, California. Participants completed a survey about abuse or household dysfunction during childhood, and multiple other health-related issues. Multivariate logistic regression was used to examine the relationships between severity of CSA (intercourse vs no intercourse) and long-term health and social problems (substance use and abuse, mental illness, and current problems with marriage and family) by gender of victim. Models controlled for exposure to other forms of adverse childhood experiences that co-occur with CSA. Among men, the relationship between the gender of the CSA perpetrator to the outcomes was also examined. RESULTS: Contact CSA was reported by 16% of males and 25% of females. Men reported female perpetration of CSA nearly 40% of the time, and women reported female perpetration of CSA 6% of the time. CSA significantly increased the risk of the outcomes. The magnitude of the increase was similar for men and women. For example, compared to reporting no sexual abuse, a history of suicide attempt was more than twice as likely among both men and women who experienced CSA (p<0.05). Compared with those who did not report CSA, men and women exposed to CSA were at a 40% increased risk of marrying an alcoholic, and a 40% to 50% increased risk of reporting current problems with their marriage (p<0.05). CONCLUSIONS: In this cohort of adult HMO members, experiencing CSA was common among both men and women. The long-term impact of CSA on multiple health and social problems was similar for both men and women. These findings strongly indicate that boys and girls are vulnerable to this form of childhood maltreatment; the similarity in the likelihood for multiple behavioral, mental, and social outcomes among men and women suggests the need to identify and treat all adults affected by CSA.

Sociogenomics: social life in molecular terms.

Spectacular progress in molecular biology, genome-sequencing projects and genomics makes this an appropriate time to attempt a comprehensive understanding of the molecular basis of social life. Promising results have already been obtained in identifying genes that influence animal social behaviour and genes that are implicated in social evolution. These findings - derived from an eclectic mix of species that show varying levels of sociality - provide the foundation for the integration of molecular biology, genomics, neuroscience, behavioural biology and evolutionary biology that is necessary for this endeavour.

Adverse childhood experiences and the risk of depressive disorders in adulthood.

BACKGROUND: Research examining the association between childhood abuse and depressive disorders has frequently assessed abuse categorically, thus not permitting discernment of the cumulative impact of multiple types of abuse. As previous research has documented that adverse childhood experiences (ACEs) are highly interrelated, we examined the association between the number of such experiences (ACE score) and the risk of depressive disorders. METHODS: Retrospective cohort study of 9460 adult health maintenance organization members in a primary care clinic in San Diego, CA who completed a survey addressing a variety of health-related concerns, which included standardized assessments of lifetime and recent depressive disorders, childhood abuse and household dysfunction. RESULTS: Lifetime prevalence of depressive disorders was 23%. Childhood emotional abuse increased risk for lifetime depressive disorders, with adjusted odds ratios (ORs) of 2.7 [95% confidence interval (CI), 2.3-3.2] in women and 2.5 (95% CI, 1.9-3.2) in men. We found a strong, dose-response relationship between the ACE score and the probability of lifetime and recent depressive disorders (P<0.0001). This relationship was attenuated slightly when a history of growing up with a mentally ill household member was included in the model, but remained significant (P<0.001). CONCLUSIONS: The number of ACEs has a graded relationship to both lifetime and recent depressive disorders. These results suggest that exposure to ACEs is associated with increased risk of depressive disorders up to decades after their occurrence. Early recognition of childhood abuse and appropriate intervention may thus play an important role in the prevention of depressive disorders throughout the life span.

Childhood Abuse, Household Dysfunction, and Indicators of Impaired Adult Worker Performance.

OBJECTIVE: We examined the relation between eight types of adverse childhood experience (ACE) and three indicators of impaired worker performance (serious job problems, financial problems, and absenteeism). METHODS: We analyzed data collected for the Adverse Childhood Experiences Study from 9633 currently employed adult members of the Kaiser Foundation Health Plan in San Diego. RESULTS: Strong graded relations were found between the ACE Score (total number of ACE categories experienced) and each measure of impaired worker performance (p < .001). We found strong evidence that the relation between ACE Score and worker performance was mediated by interpersonal relationship problems, emotional distress, somatic symptoms, and substance abuse. CONCLUSIONS: The long-term effects of adverse childhood experiences on the workforce impose major human and economic costs that are preventable. These costs merit attention from the business community in conjunction with specialists in occupational medicine and public health.

Gene expression profiles in the brain predict behavior in individual honey bees.

We show that the age-related transition by adult honey bees from hive work to foraging is associated with changes in messenger RNA abundance in the brain for 39% of approximately 5500 genes tested. This result, discovered using a highly replicated experimental design involving 72 microarrays, demonstrates more extensive genomic plasticity in the adult brain than has yet been shown. Experimental manipulations that uncouple behavior and age revealed that messenger RNA changes were primarily associated with behavior. Individual brain messenger RNA profiles correctly predicted the behavior of 57 out of 60 bees, indicating a robust association between brain gene expression in the individual and naturally occurring behavioral plasticity.